Inbreeding is an inevitable outcome of artificial selection. Inbreeding depression estimation has been measured successfully with pedigrees; but we propose that the utility of this measurement could be improves using a molecular pedigree based on high density SNP genotype information. Such information is a resource to calculate runs of homozygosity (ROH) that assist identification of recessive mutations underlying complex traits. Negative correlations between a trait of interest, particularly daughter pregnancy rate (DPR) and somatic cell score (SCS) and autozygosity are suggested as evidence of inbreeding depression in dairy cattle. Therefore we examined ROH in regions of at least 50 SNP (corresponding to > 500Kb to detect association with fertility, somatic cell score and genomic autozygosity in Holsteins and Jerseys. In addition, relationships between local ROH and inbreeding coefficient (F) were assessed to evaluate genomic regions associated with increased inbreeding. Then associations of ROH with F, DPR and SCS were compared between contemporary Holsteins groups and those unselected for improved milk production during last 50 years. Only 3 ROH were significantly associated with F in the unselected Holstein group, whereas selection has contributed greatly to increase F in local chromosomal regions. Genomic autozygosity on chromosome 1, 3, 8, 12, 15, 16, 20, 23 and 26 were associated with DPR, and influenced SCS on chromosomes 4, 8, 10, 11, 14, 19 and 23. In contrast to selected group, high ROH did not reduce DPR or increase SCS in unselected Holsteins. In Jerseys, Over 25 genomic ROH regions were positively and significantly associated with F suggesting haplotype sharing derived from commons ancestors was not equally distributed across the genome. Genomic autozygosity was associated with reduced DPR on chromosomes 3 and 5, and increased SCS significantly on chromosomes 1, 4, 17, 20 and 21 in Jerseys. In most chromosomes of selected Holsteins and Jerseys, ROHs positively and significantly associated with F were found, indicating that haplotype sharing from common ancestors is not equally distributed across the genome. However, correlation between local effect of autozygosity on inbreeding depression and ROH associated with F was not clearly identified in Jerseys and Holsteins. In summary, genomic homozygosity has increased as F elevated due to selection, but restricted local effects of autozygosity affected fertility and SCS in dairy cattle, whereas inbreeding depression appears to be correlated with overall F.